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Article ID: 802 - Last Modified: December 4, 2010

When defining positional constraints in Glide, how do I tell which is atom number 1, atom number 2, and so on?

The atoms are numbered as they appear in the SMARTS pattern, from left to right. So in the pattern

[#1][*C-0X4*]([#1])[S-0X4](=[O-0X1])=[O-0X1]

the methyl carbon is atom number 2. The numbers that you put in the Numbers text box are the indices in the pattern, not the atom numbers in the ligand structure (as you'd see when displaying the atom numbers in the Maestro Workspace). So the '2' for the methyl carbon applies to all ligands.

Keywords: positional constraints, atom numbering, Glide

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